biologically meaningful. This criterion is different from that used for the ALIGATOR analysis of GWAS data (two significant genes) for two reasons. First, each gene is counted only once in ALIGATOR but can be counted multiple times in the CNV analysis (if hit by multiple CNVs). Second, two significant genes may be sufficient to flag a pathway of interest in a GWAS context if these gene associations are sufficiently significant. Correction for multiple testing was applied by randomly permuting case/control status of CNVs and repeating the analysis 5,000 times. This procedure gave a corrected p value for enrichment of gene hits in case CNVs for each gene set as well as a test of whether more gene sets than expected are significantly enriched. The latter gives a test of overlap in the pathways enriched for rare CNVs and common associated SNPs.
